SerraNA: nucleic acids elasticity from simulations

The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that infers elastic parameters of double-stranded nucleic acids from bp length up to the whole molecule using ensembles from numerical simulations. Estimations of bulk elastic constants are in general agreement with experiments, although the static persistence length and stretch modulus parameters are more challenging to calculate due to DNA chirality and vibrations at the ends. The program also reveals that a soft persistence length is built up from local periodic bending angles in phase with the DNA helicoidal shape. The whole set of 136 tetra-bp combinations present big differences in all elastic constants of over 200% demonstrating the importance of sequence. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA.

V Velasco-Berrelleza, M Burman, JW Shepherd, MC Leake, R Golestanian and A Noy (2020). “SerraNA: a program to determine nucleic acids elasticity from simulation data” Phys Chem Chem Phys, 22, 19254-19266, https://doi.org/10.1039/D0CP02713H

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